Blixem

Blixem visualizes multiple sequence alignments and BLAST (Basic Local Alignment Search Tool) search results to support analysis of DNA sequences and protein similarities from genome sequencing projects.

Key Features:

• Multiple sequence alignment visualization: Provides graphical representation of multiple sequence alignments for inspection of matches and alignment patterns.
• BLAST integration: Displays results produced by BLAST suite programs for downstream visual analysis.
• MSPcrunch compatibility: Accepts MSPcrunch-processed results where biased compositions and redundant matches are removed while weak matches consistent with larger gapped alignments are preserved.
• Three-frame translated alignment: Aligns matches to a translated DNA query sequence across three reading frames.
• Match distribution display: Visualizes the spatial distribution of matches along the entire length of the DNA query.
• Large dataset handling: Capable of visualizing alignments for large genomic datasets, exemplified by analysis of 36 C. elegans cosmid clones totaling 1.2 megabases.

Scientific Applications:

• Evaluation of protein similarities: Supports assessment of protein matches identified through BLAST searches.
• Genome sequencing analysis: Aids analysis of extensive DNA sequences generated by genome sequencing projects.
• Comparative genomics: Facilitates comparison of sequence alignments and distribution patterns across genomic regions.
• Detection of distant similarities: Enables inspection of weak matches preserved by MSPcrunch that may indicate distant homologous relationships.

Methodology:

Displays BLAST suite search results and visualizes multiple sequence alignments; accepts MSPcrunch-processed results that remove biased compositions and redundant matches while preserving weak matches consistent with larger gapped alignments; aligns matches to a translated DNA query sequence across three reading frames and shows their distribution along the query.